running the installer for version 3.2 to upgrade from version 3.0. when i get the base Monitor port number test, it says the port is unavailable. This is obviously true since the old install is using it. Am i missing a step here? is the installer not able to pick up the older version and upgrade it?

The installer stops and disables the old version but if something is keeping a handle on the service, it is unable to overwrite with the new version. The services.msc app is particularly annoying in this respect. If that's open then close it and retry the installation.

I have seen the issue but it always seems to resolve itself. Are you still having problems?

Our installer just overwrites the existing files. The only real 'upgrade' done is to the data repository. The way this works could definitely be improved.

What version of IIS have you got out of interest? As far as I'm aware, the IIS auto-detection has worked fairly well in the past.

Would it be possible for check services.msc to see if "SQL Monitor 3 Base Monitor" is still running? If it is it could be worth stopping it before retrying the installer. The installer should be disabling this service but it doesn't appear to be working correctly in your case.